Analyses of the NAC transcription factor gene family in Gossypium raimondii Ulbr.: chromosomal location, structure, phylogeny, and expression patterns

Genome-Wide Identification, Characterization, and Expression Analysis of the NAC Transcription Factor Family in Sweet Cherry (Prunus avium L.)

The NAC (NAM, ATAF1/2, and CUC2) family is one of the largest plant-specific transcription factor families, playing a crucial role in adaptation to abiotic stresses. However, the NAC gene family in sweet cherry (Prunus avium L.) remains poorly understood. In this study, we identified 130 NAC genes (PaNAC) from the sweet cherry genome, which were unevenly distributed across eight chromosomes. Phylogenetic analysis classified the PaNACs into 21 distinct groups, including 2 sweet cherry-specific groups. Comparative analysis revealed significant variations in gene proportions, exon-intron structures, and motif compositions among different groups. Furthermore, cis-element analysis suggested the potential roles of PaNACs in regulating plant growth, development, hormone signaling, and stress responses. Transcriptomic data revealed tissue-specific expression patterns for several PaNAC genes. qRT-PCR further confirmed that eight selected PaNACs were responsive to various abiotic stresses in Gisela 6, a widely used hybrid rootstock in sweet cherry production that shares high sequence similarity in NAC genes with P. avium. These findings provide valuable insights for future research on the functional characteristics of the PaNAC genes in the growth, development, and responses to abiotic stress in sweet cherry.

NAC transcription factors as biological macromolecules responded to abiotic stress: A comprehensive review

NAC transcription factors (NAC TFs) represent a large and vital family of transcription factors in the plant kingdom, playing a central role in regulating plant growth, developmental processes, and responses to abiotic stresses. As key regulators, NAC TFs fine-tune the expression of downstream genes, thereby actively contributing to the adaptation of crops to various abiotic stresses. The functions of NAC TFs are controlled by several complex signaling pathways, including those involving phytohormones (such as abscisic acid (ABA) and ethylene (ET)), reactive oxygen species (ROS), and mitogen-activated protein kinases (MAPKs). This review highlights recent advances in the biological functions and signaling pathways of NAC TFs in crops under abiotic stress conditions, such as drought, salinity, and extreme temperatures. It also offers prospects for further exploration of the complex mechanisms by which NAC TFs operate within signaling networks, with the aim of developing food crops with enhanced physiological traits.

Computational analysis and expression profiling of NAC transcription factor family involved in biotic stress response in Manihot esculenta

The Nascent polypeptide-Associated Complex (NAC) family is among the largest plant-specific TF families and plays an important role in plant growth, development, and stress responses. NAC TFs have been extensively studied in plants such as rice and Arabidopsis; however, their characterization, functions, evolution, and expression patterns in Manihot esculenta (cassava) under environmental stress remain largely unexplored. Here, we used bioinformatic analyses and biotic stress responses to investigate the physicochemical properties, chromosome location, phylogeny, gene structure, expression patterns, and cis-elements in promoter regions of the NAC TFs in cassava. We identified 119 M. esculenta NAC (MeNAC) gene families, unevenly distributed on 16 chromosomes. We investigated expression patterns of all identified MeNAC TFs under Xanthomonas axonopodis pv. manihotis (Xam) infection, strain CHN11, at different time points. Only 20 MeNAC TFs showed expression of significant bacterial resistance. Six MeNACs (MeNAC7, 26, 63, 65, 77, and 113) were selected for functional analysis. qRT-PCR assays revealed that MeNAC7, 26, 63, 65, 77, and 113 were induced in response to XamCHN11 infection and may participate in the molecular interaction of cassava and bacterial blight. Interestingly, MeNAC26, MeNAC63, MeNAC65, and MeNAC113 responded to XamCHN11 infection at 3 h post-inoculation. Furthermore, we identified 13 stress-related cis-elements in promoter regions of the MeNAC genes that are involved in diverse environmental stress responses. Phylogenetic analysis revealed that MeNAC genes with similar structures and motif distributions were grouped. This study provides valuable insights into the evolution, diversity, and characterization of MeNAC TFs. It lays the groundwork for a better understanding of their biological roles and molecular mechanisms in cassava.

Integrative Analysis of Transcriptome and Metabolome Reveals the Pivotal Role of the NAM Family Genes in Oncidium hybridum Lodd. Pseudobulb Growth

Oncidium hybridum Lodd. is an important ornamental flower that is used as both a cut flower and a potted plant around the world; additionally, its pseudobulbs serve as essential carriers for floral organs and flower development. The NAM gene family is crucial for managing responses to various stresses as well as regulating growth in plants. However, the mechanisms by which NAM genes regulate the development of pseudobulbs remain unclear. In this study, a total of 144 NAM genes harboring complete structural domains were identified in O. hybridum. The 144 NAM genes were systematically classified into 14 distinct subfamilies via phylogenetic analysis. Delving deeper into the conserved motifs revealed that motifs 1-6 exhibited remarkable conservation, while motifs 7-10 presented in a few NAM genes only. Notably, NAM genes sharing identical specific motifs were classified into the same subfamily, indicating functional relatedness. Furthermore, the examination of occurrences of gene duplication indicated that the NAM genes display 16 pairs of tandem duplications along with five pairs of segmental duplications, suggesting their role in genetic diversity and potential adaptive evolution. By conducting a correlation analysis integrating transcriptomics and metabolomics at four stages of pseudobulb development, we found that OhNAM023, OhNAM030, OhNAM007, OhNAM019, OhNAM083, OhNAM047, OhNAM089, and OhNAM025 exhibited significant relationships with the endogenous plant hormones jasmonates (JAs), hinting at their potential involvement in hormonal signaling. Additionally, OhNAM089, OhNAM025, OhNAM119, OhNAM055, and OhNAM136 showed strong links with abscisic acid (ABA) and abscisic acid glucose ester (ABA-GE), suggesting the possible regulatory function of these NAM genes in plant growth and stress responses. The 144 NAM genes identified in this study provide a basis for subsequent research and contribute to elucidating the intricate molecular mechanisms of NAM genes in Oncidium and potentially in other species.

Genome-wide identification of HSP90 gene family in Rosa chinensis and its response to salt and drought stresses

Heat shock protein 90 (HSP90) is important for many organisms, including plants. Based on the whole genome information, the gene number, gene structure, evolutionary relationship, protein structure, and active site of the HSP90 gene family in Rosa chinensis and Rubus idaeus were determined, and the expression of the HSP90 gene under salt, and drought stresses in two rose varieties Wangxifeng and Sweet Avalanche were analyzed. Six and eight HSP90 genes were identified from R. chinensis and Ru. idaeus, respectively. Phylogenetic analysis revealed that the analyzed genes were divided into two Groups and four subgroups (Classes 1a, 1b, 2a, and 2b). Although members within the same classes displayed highly similar gene structures, while the gene structures and conserved domains of Group 1 (Class 1a and 1b) and the Group 2 (Class 2a and 2b) are different. Tandem and segmental duplication genes were found in Ru. idaeus, but not in R. chinensis, perhaps explaining the difference in HSP90 gene quantity in the two analyzed species. Analysis of cis-acting elements revealed abundant abiotic stress, photolight-response, and hormone-response elements in R. chinensis HSP90s. qRT-PCR analysis suggested that RcHSP90-1-1, RcHSP90-5-1 and RcHSP90-6-1 in Sweet Avalanche and Wangxifeng varieties played important regulatory roles under salt and drought stress. The analysis of protein structure and active sites indicate that the potential different roles of RcHSP90-1-1, RcHSP90-5-1, and RcHSP90-6-1 in salt and drought stresses may come from the differences of corresponding protein structures and activation sites. These data will provide information for the breeding of rose varieties with high stress resistance.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-04052-0.

Genome-Wide Identification of NAC Family Genes and Their Expression Analyses in Response to Osmotic Stress in Cannabis sativa L

NAC (NAM, ATAF1/2, and CUC2) transcription factors are unique and essential for plant growth and development. Although the NAC gene family has been identified in a wide variety of plants, its chromosomal location and function in Cannabis sativa are still unknown. In this study, a total of 69 putative CsNACs were obtained, and chromosomal location analysis indicated that the CsNAC genes mapped unevenly to 10 chromosomes. Phylogenetic analyses showed that the 69 CsNACs could be divided into six subfamilies. Additionally, the CsNAC genes in group IV-a are specific to Cannabis sativa and contain a relatively large number of exons. Promoter analysis revealed that most CsNAC promoters contained cis-elements related to plant hormones, the light response, and abiotic stress. Furthermore, transcriptome expression profiling revealed that 24 CsNAC genes in two Cannabis sativa cultivars (YM1 and YM7) were significantly differentially expressed under osmotic stress, and these 12 genes presented differential expression patterns across different cultivars according to quantitative real-time PCR (RT-qPCR) analysis. Among these, the genes homologous to the CsNAC18, CsNAC24, and CsNAC61 genes have been proven to be involved in the response to abiotic stress and might be candidate genes for further exploration to determine their functions. The present study provides a comprehensive insight into the sequence characteristics, structural properties, evolutionary relationships, and expression patterns of NAC family genes under osmotic stress in Cannabis sativa and provides a basis for further functional characterization of CsNAC genes under osmotic stress to improve agricultural traits in Cannabis sativa.

Genomic organization and expression profiles of nitrogen assimilation genes in Glycine max

Background

Glutamine synthetase (GS), glutamate synthase (GOGAT), and nitrate reductase (NR) are key enzymes involved in nitrogen assimilation and metabolism in plants. However, the systematic analysis of these gene families lacked reports in soybean (Glycine max (L.) Merr.), one of the most important crops worldwide.

Methods

In this study, we performed genome-wide identification and characterization of GS, GOGAT, and NR genes in soybean under abiotic and nitrogen stress conditions.

Results

We identified a total of 10 GS genes, six GOGAT genes, and four NR genes in the soybean genome. Phylogenetic analysis revealed the presence of multiple isoforms for each gene family, indicating their functional diversification. The distribution of these genes on soybean chromosomes was uneven, with segmental duplication events contributing to their expansion. Within the nitrogen assimilation genes (NAGs) group, there was uniformity in the exon-intron structure and the presence of conserved motifs in NAGs. Furthermore, analysis of cis-elements in NAG promoters indicated complex regulation of their expression. RT-qPCR analysis of seven soybean NAGs under various abiotic stresses, including nitrogen deficiency, drought-nitrogen, and salinity, revealed distinct regulatory patterns. Most NAGs exhibited up-regulation under nitrogen stress, while diverse expression patterns were observed under salt and drought-nitrogen stress, indicating their crucial role in nitrogen assimilation and abiotic stress tolerance. These findings offer valuable insights into the genomic organization and expression profiles of GS, GOGAT, and NR genes in soybean under nitrogen and abiotic stress conditions. The results have potential applications in the development of stress-resistant soybean varieties through genetic engineering and breeding.

Pangenome characterization and analysis of the NAC gene family reveals genes for Sclerotinia sclerotiorum resistance in sunflower (Helianthus annuus)

BACKGROUND

Sunflower (Helianthus annuus) is one of the most important economic crops in oilseed production worldwide. The different cultivars exhibit variability in their resistance genes. The NAC transcription factor (TF) family plays diverse roles in plant development and stress responses. With the completion of the H. annuus genome sequence, the entire complement of genes coding for NACs has been identified. However, the reference genome of a single individual cannot cover all the genetic information of the species.

RESULTS

Considering only a single reference genome to study gene families will miss many meaningful genes. A pangenome-wide survey and characterization of the NAC genes in sunflower species were conducted. In total, 139 HaNAC genes are identified, of which 114 are core and 25 are variable. Phylogenetic analysis of sunflower NAC proteins categorizes these proteins into 16 subgroups. 138 HaNACs are randomly distributed on 17 chromosomes. SNP-based haplotype analysis shows haplotype diversity of the HaNAC genes in wild accessions is richer than in landraces and modern cultivars. Ten HaNAC genes in the basal stalk rot (BSR) resistance quantitative trait loci (QTL) are found. A total of 26 HaNAC genes are differentially expressed in response to Sclerotinia head rot (SHR). A total of 137 HaNAC genes are annotated in Gene Ontology (GO) and are classified into 24 functional groups. GO functional enrichment analysis reveals that HaNAC genes are involved in various functions of the biological process.

CONCLUSIONS

We identified NAC genes in H. annuus (HaNAC) on a pangenome-wide scale and analyzed S. sclerotiorum resistance-related NACs. This study provided a theoretical basis for further genomic improvement targeting resistance-related NAC genes in sunflowers.

Genome-wide identification of the B3 transcription factor family in pepper (Capsicum annuum) and expression patterns during fruit ripening

In plants, B3 transcription factors play important roles in a variety of aspects of their growth and development. While the B3 transcription factor has been extensively identified and studied in numerous species, there is limited knowledge regarding its B3 superfamily in pepper. Through the utilization of genome-wide sequence analysis, we identified a total of 106 B3 genes from pepper (Capsicum annuum), they are categorized into four subfamilies: RAV, ARF, LAV, and REM. Chromosome distribution, genetic structure, motif, and cis-acting element of the pepper B3 protein were analyzed. Conserved gene structure and motifs outside the B3 domain provided strong evidence for phylogenetic relationships, allowing potential functions to be deduced by comparison with homologous genes from Arabidopsis. According to the high-throughput transcriptome sequencing analysis, expression patterns differ during different phases of fruit development in the majority of the 106 B3 pepper genes. By using qRT-PCR analysis, similar expression patterns in fruits from various time periods were discovered. In addition, further analysis of the CaRAV4 gene showed that its expression level decreased with fruit ripening and located in the nucleus. B3 transcription factors have been genome-wide characterized in a variety of crops, but the present study is the first genome-wide analysis of the B3 superfamily in pepper. More importantly, although B3 transcription factors play key regulatory roles in fruit development, it is uncertain whether B3 transcription factors are involved in the regulation of the fruit development and ripening process in pepper and their specific regulatory mechanisms because the molecular mechanisms of the process have not been fully explained. The results of the study provide a foundation and new insights into the potential regulatory functions and molecular mechanisms of B3 genes in the development and ripening process of pepper fruits, and provide a solid theoretical foundation for the enhancement of the quality of peppers and their selection and breeding of high-yield varieties.

Genome-Wide Identification of NAC Gene Family and Expression Analysis under Abiotic Stresses in Avena sativa

In this study, a total of 177 NAC members were identified in Avena sativa, located on 21 chromosomes. Phylogenetic analysis showed that AsNAC proteins could be divided into seven subfamilies (I-VII), and that proteins in the same subfamily have similar protein motifs. Gene structure analysis found that NAC introns ranged from 1 to 17. Cis-element analysis of the promoter indicated that the gene family may have stress-related elements and growth regulation elements. Through qRT-PCR experiments, we speculated that AsNACs genes can respond to abiotic stresses such as cold, freezing, salt, and saline alkali. This study provides a theoretical basis for further exploring the function of the NAC gene family in A. sativa.

NAC domain transcription factor gene GhNAC3 confers drought tolerance in plants

Abiotic stress seriously affects the growth, yield, and fiber quality of cotton. It is of great importance to cultivate drought-resistant and salt-tolerant cotton. NAC (NAM, ATAF1/2, and CUC2) is a plant-specific transcription factor, which is widely involved in the response to abiotic stress. Here, we discovered the GhNAC3 gene isolated from the expression profile of drought stress in cotton and verified its functions in cotton. First, GhNAC3 was strongly induced expression by drought and salt stresses. Gene structure analysis revealed that GhNAC3 had a conserved NAC domain and was homologous to several stress-related NAC transcription factors gene of Arabidopsis. Subcellular localization and transcriptional activation assays revealed that GhNAC3 was a nuclear protein with a C-terminal transcriptional activation domain. Overexpression of GhNAC3 enhanced Arabidopsis tolerance to drought stress with reduced sensitivity to ABA, characterized by increased germination and cotyledon rates under drought stress, and promoted root elongation. VIGS silencing of GhNAC3 reduced cotton tolerance to drought stress as indicated by the low water content of the leaves under drought treatment, significantly faster water loss and lower ABA content in detached leaves, along with the accumulation of more hydrogen peroxide (H₂O₂) and malondialdehyde (MDA). In conclusion, GhNAC3 plays an important role in the abiotic stress of cotton, which might have great application potential in molecular breeding of cotton varieties with drought resistance.

Divergent Response Strategies of CsABF Facing Abiotic Stress in Tea Plant: Perspectives From Drought-Tolerance Studies

In plants, the bZIP family plays vital roles in various biological processes, including seed maturation, flower development, light signal transduction, pathogen defense, and various stress responses. Tea, as a popular beverage, is widely cultivated and has withstood a degree of environmental adversity. Currently, knowledge of the bZIP gene family in tea plants remains very limited. In this study, a total of 76 CsbZIP genes in tea plant were identified for the whole genome. Phylogenetic analysis with Arabidopsis counterparts revealed that CsbZIP proteins clustered into 13 subgroups, among which 13 ABFs related to the ABA signaling transduction pathway were further identified by conserved motif alignment and named CsABF1-13, these belonged to the A and S subgroups of CsbZIP and had close evolutionary relationships, possessing uniform or similar motif compositions. Transcriptome analysis revealed the expression profiles of CsABF genes in different tissues (bud, young leaf, mature leaf, old leaf, stem, root, flower, and fruit) and under diverse environmental stresses (drought, salt, chilling, and MeJA). Several CsABF genes with relatively low tissue expression, including CsABF1, CsABF5, CsABF9, and CsABF10, showed strong expression induction in stress response. Thirteen CsABF genes, were examined by qRT-PCR in two tea plant cultivars, drought-tolerant "Taicha 12" and drought-sensitive "Fuyun 6", under exogenous ABA and drought stress. Furthermore, CsABF2, CsABF8, and CsABF11, were screened out as key transcription factors regulating drought tolerance of tea cultivars. Subsequently, some potential target genes regulated by CsABFs were screened by co-expression network and enrichment analysis. This study update CsbZIP gene family and provides a global survey of the ABF gene family in tea plant. The resolution of the molecular mechanism of drought resistance in different varieties could be helpful for improving stress resistance in tea plant via genetic engineering.

Genome-wide characterization and expression profiling of B3 superfamily during ethylene-induced flowering in pineapple (Ananas comosus L.)

BACKGROUND

The B3 superfamily (B3s) represents a class of large plant-specific transcription factors, which play diverse roles in plant growth and development process including flowering induction. However, identification and functional surveys of B3 superfamily have not been reported in ethylene-induced pineapple flowering (Ananas comosus).

RESULTS

57 B3 genes containing B3 domain were identified and phylogenetically classified into five subfamilies. Chromosomal localization analysis revealed that 54 of 57 AcB3s were located on 21 Linkage Groups (LG). Collinearity analysis demonstrated that the segmental duplication was the main event in the evolution of B3 gene superfamily, and most of them were under purifying selection. The analysis of cis-element composition suggested that most of these genes may have function in response to abscisic acid, ethylene, MeJA, light, and abiotic stress. qRT-PCR analysis of 40 AcB3s containing ethylene responsive elements exhibited that the expression levels of 35 genes were up-regulated within 1 d after ethephon treatment and some were highly expressed in flower bud differentiation period in stem apex, such as Aco012003, Aco019552 and Aco014401.

CONCLUSION

This study provides a basic information of AcB3s and clues for involvement of some AcB3s in ethylene-induced flowering in pineapple.

ThNAC12 from Tamarix hispida directly regulates ThPIP2;5 to enhance salt tolerance by modulating reactive oxygen species

NAC (NAM, ATAF1/2 and CUC2) transcription factors play critical roles in plant development and abiotic stress responses, and aquaporins have diverse functions in environmental stress responses. In this study, we described the salt-induced transcriptional responses of ThNAC12 and ThPIP2;5 in Tamarix hispida, and their regulatory mechanisms in response to salt stress. Using yeast one-hybrid (Y1H), chromatin immunoprecipitation (ChIP) and dual-luciferase reporter assays, we identified that ThNAC12 directly binds to the NAC recognition sequence (NACRS) of the ThPIP2;5 promoter and then activates the ThPIP2;5 expression. Subcellular localization and transcriptional activation assays demonstrated that ThNAC12 was a nuclear protein with a C-terminal transactivation domain. Compared with the corresponding control plants, transgenic plants overexpressing ThNAC12 exhibited enhanced salt tolerance and displayed increased reactive oxygen species (ROS) scavenging capability and antioxidant enzyme activity levels under salt stress. All results suggested that overexpression of ThNAC12 in plants enhanced salt tolerance through modulation of ROS scavenging via direct regulation of ThPIP2;5 expression in T. hispida.

Gene Expression Correlation Analysis Reveals MYC-NAC Regulatory Network in Cotton Pigment Gland Development

Plant NAC (NAM, ATAF1/2, and CUC2) family is involved in various development processes including Programmed Cell Death (PCD) associated development. However, the relationship between NAC family and PCD-associated cotton pigment gland development is largely unknown. In this study, we identified 150, 153 and 299 NAC genes in newly updated genome sequences of G. arboreum, G. raimondii and G. hirsutum, respectively. All NAC genes were divided into 8 groups by the phylogenetic analysis and most of them were conserved during cotton evolution. Using the vital regulator of gland formation GhMYC2-like as bait, expression correlation analysis screened out 6 NAC genes which were low-expressed in glandless cotton and high-expressed in glanded cotton. These 6 NAC genes acted downstream of GhMYC2-like and were induced by MeJA. Silencing CGF1(Cotton Gland Formation1), another MYC-coding gene, caused almost glandless phenotype and down-regulated expression of GhMYC2-like and the 6 NAC genes, indicating a MYC-NAC regulatory network in gland development. In addition, predicted regulatory mechanism showed that the 6 NAC genes were possibly regulated by light, various phytohormones and transcription factors as well as miRNAs. The interaction network and DNA binding sites of the 6 NAC transcription factors were also predicted. These results laid the foundation for further study of gland-related genes and gland development regulatory network.

The biotechnological importance of the plant-specific NAC transcription factor family in crop improvement

Climate change, malnutrition, and food insecurity are the inevitable challenges being faced by the agriculture sector today. Plants are susceptible to extreme temperatures during the crucial phases of flowering and seed development, and elevated carbon levels also lead to yield losses. Productivity is also affected by floods and droughts. Therefore, increasing plant yield and stress tolerance are the priorities to be met through novel biotechnological interventions. The contributions of NAC genes towards enhancing plant survivability under stress is well known. Here we focus on the potential of NAC genes in the regulation of abiotic stress tolerance, secondary cell wall synthesis, lateral root development, yield potential, seed size and biomass, ROS signaling, leaf senescence, and programmed cell death. Once naturally tolerant candidate NAC genes have been identified, and the nature of their association with growth and fitness against multi-environmental stresses has been determined, they can be exploited for building inherent tolerance in future crops via transgenic technologies. An update on the latest developments is provided in this review, which summarizes the current understanding of the roles of NAC in the establishment of various stress-adaptive mechanisms in model and food crop plants.

Comprehensive analysis and identification of drought-responsive candidate NAC genes in three semi-arid tropics (SAT) legume crops

Background

Chickpea, pigeonpea, and groundnut are the primary legume crops of semi-arid tropics (SAT) and their global productivity is severely affected by drought stress. The plant-specific NAC (NAM - no apical meristem, ATAF - Arabidopsis transcription activation factor, and CUC - cup-shaped cotyledon) transcription factor family is known to be involved in majority of abiotic stresses, especially in the drought stress tolerance mechanism. Despite the knowledge available regarding NAC function, not much information is available on NAC genes in SAT legume crops.

Results

In this study, genome-wide NAC proteins – 72, 96, and 166 have been identified from the genomes of chickpea, pigeonpea, and groundnut, respectively, and later grouped into 10 clusters in chickpea and pigeonpea, while 12 clusters in groundnut. Phylogeny with well-known stress-responsive NACs in Arabidopsis thaliana, Oryza sativa (rice), Medicago truncatula, and Glycine max (soybean) enabled prediction of putative stress-responsive NACs in chickpea (22), pigeonpea (31), and groundnut (33). Transcriptome data revealed putative stress-responsive NACs at various developmental stages that showed differential expression patterns in the different tissues studied. Quantitative real-time PCR (qRT-PCR) was performed to validate the expression patterns of selected stress-responsive, Ca_NAC (Cicer arietinum - 14), Cc_NAC (Cajanus cajan - 15), and Ah_NAC (Arachis hypogaea - 14) genes using drought-stressed and well-watered root tissues from two contrasting drought-responsive genotypes of each of the three legumes. Based on expression analysis, Ca_06899, Ca_18090, Ca_22941, Ca_04337, Ca_04069, Ca_04233, Ca_12660, Ca_16379, Ca_16946, and Ca_21186; Cc_26125, Cc_43030, Cc_43785, Cc_43786, Cc_22429, and Cc_22430; Ah_ann1.G1V3KR.2, Ah_ann1.MI72XM.2, Ah_ann1.V0X4SV.1, Ah_ann1.FU1JML.2, and Ah_ann1.8AKD3R.1 were identified as potential drought stress-responsive candidate genes.

Conclusion

As NAC genes are known to play role in several physiological and biological activities, a more comprehensive study on genome-wide identification and expression analyses of the NAC proteins have been carried out in chickpea, pigeonpea and groundnut. We have identified a total of 21 potential drought-responsive NAC genes in these legumes. These genes displayed correlation between gene expression, transcriptional regulation, and better tolerance against drought. The identified candidate genes, after validation, may serve as a useful resource for molecular breeding for drought tolerance in the SAT legume crops.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07602-5.

Comprehensive analysis of NAC transcription factor family uncovers drought and salinity stress response in pearl millet (Pennisetum glaucum)

BACKGROUND

Pearl millet (Pennisetum glaucum) is a cereal crop that possesses the ability to withstand drought, salinity and high temperature stresses. The NAC [NAM (No Apical Meristem), ATAF1 (Arabidopsis thaliana Activation Factor 1), and CUC2 (Cup-shaped Cotyledon)] transcription factor family is one of the largest transcription factor families in plants. NAC family members are known to regulate plant growth and abiotic stress response. Currently, no reports are available on the functions of the NAC family in pearl millet.

RESULTS

Our genome-wide analysis found 151 NAC transcription factor genes (PgNACs) in the pearl millet genome. Thirty-eight and 76 PgNACs were found to be segmental and dispersed duplicated respectively. Phylogenetic analysis divided these NAC transcription factors into 11 groups (A-K). Three PgNACs (- 073, - 29, and - 151) were found to be membrane-associated transcription factors. Seventeen other conserved motifs were found in PgNACs. Based on the similarity of PgNACs to NAC proteins in other species, the functions of PgNACs were predicted. In total, 88 microRNA target sites were predicted in 59 PgNACs. A previously performed transcriptome analysis suggests that the expression of 30 and 42 PgNACs are affected by salinity stress and drought stress, respectively. The expression of 36 randomly selected PgNACs were examined by quantitative reverse transcription-PCR. Many of these genes showed diverse salt- and drought-responsive expression patterns in roots and leaves. These results confirm that PgNACs are potentially involved in regulating abiotic stress tolerance in pearl millet.

CONCLUSION

The pearl millet genome contains 151 NAC transcription factor genes that can be classified into 11 groups. Many of these genes are either upregulated or downregulated by either salinity or drought stress and may therefore contribute to establishing stress tolerance in pearl millet.

Genome-Wide Identification and Gene Expression Analysis of Acyl-Activating Enzymes Superfamily in Tomato (Solanum lycopersicum) Under Aluminum Stress

In response to changing environments, plants regulate gene expression and subsequent metabolism to acclimate and survive. A superfamily of acyl-activating enzymes (AAEs) has been observed in every class of creatures on planet. Some of plant AAE genes have been identified and functionally characterized to be involved in growth, development, biotic, and abiotic stresses via mediating diverse metabolic pathways. However, less information is available about AAEs superfamily in tomato (Solanum lycopersicum), the highest value fruit and vegetable crop globally. In this study, we aimed to identify tomato AAEs superfamily and investigate potential functions with respect to aluminum (Al) stress that represents one of the major factors limiting crop productivity on acid soils worldwide. Fifty-three AAE genes of tomato were identified and named on the basis of phylogenetic relationships between Arabidopsis and tomato. The phylogenetic analysis showed that AAEs could be classified into six clades; however, clade III contains no AAE genes of tomato. Synteny analyses revealed tomato vegetable paralogs and Arabidopsis orthologs. The RNA-seq and quantitative reverse-transcriptase PCR (qRT-PCR) analysis indicated that 9 out of 53 AAEs genes were significantly up- or downregulated by Al stress. Numerous cis-acting elements implicated in biotic and abiotic stresses were detected in the promoter regions of SlAAEs. As the most abundantly expressed gene in root apex and highly induced by Al, there are many potential STOP1 cis-acting elements present in the promoter of SlAAE3-1, and its expression in root apex was specific to Al. Finally, transgenic tobacco lines overexpressing SlAAE3-1 displayed increased tolerance to Al. Altogether, our results pave the way for further studies on the functional characterization of SlAAE genes in tomato with a wish of improvement in tomato crop in the future.

NAC Transcription Factors as Positive or Negative Regulators during Ongoing Battle between Pathogens and Our Food Crops

The NAC (NAM, ATAF1/2, and CUC2) family of proteins is one of the largest plant-specific transcription factor (TF) families and its members play varied roles in plant growth, development, and stress responses. In recent years, NAC TFs have been demonstrated to participate in crop-pathogen interactions, as positive or negative regulators of the downstream defense-related genes. NAC TFs link signaling pathways between plant hormones, including salicylic acid (SA), jasmonic acid (JA), ethylene (ET), and abscisic acid (ABA), or other signals, such as reactive oxygen species (ROS), to regulate the resistance against pathogens. Remarkably, NAC TFs can also contribute to hypersensitive response and stomatal immunity or can be hijacked as virulence targets of pathogen effectors. Here, we review recent progress in understanding the structure, biological functions and signaling networks of NAC TFs in response to pathogens in several main food crops, such as rice, wheat, barley, and tomato, and explore the directions needed to further elucidate the function and mechanisms of these key signaling molecules.

Large-Scale Cloning and Comparative Analysis of TaNAC Genes in Response to Stripe Rust and Powdery Mildew in Wheat (Triticum aestivum L.)

The NAM, ATAF1/2, and CUC2 (NAC) transcription factors (TFs) constitute the largest plant-specific TF superfamily, and play important roles in various physiological processes, including stress responses. Stripe rust and powdery mildew are the most damaging of the fungal diseases that afflict wheat (Triticum aestivum L.). However, studies on Triticum aestivum NAC (TaNAC)s’ role in resistance to the two diseases are still limited, especially in an overall comparative analysis of TaNACs responding or not to fungal stress. In the present study, 186 TaNAC transcripts were obtained from the resistant hexaploid wheat line N9134 under fungal stress, and 180 new transcripts were submitted to GenBank. Statistical results show that 35.1% (54/154) of TaNAC genes responded to stripe rust and powdery mildew in the seedling stage. “Abnormal” coding transcripts of differentially expressed (DE)-TaNAC genes in wheat responding to fungal stress were found in a significantly higher proportion (24/117 vs. 8/69, p = 0.0098) than in non-DE-NACs. This hinted that the alternative splicing of TaNAC genes was active in transcriptional or post-transcriptional regulation during plant-pathogen interactions. Full-length NAC proteins were classified into nine groups via phylogenetic analysis. Multiple-sequence alignment revealed diversity in the C-terminal structural organization, but the differentially expressed gene (DEG)-encoding proteins enriched in Subgroups VI and VII were conserved, with WV[L/V]CR amino acid residues in Motif 7 following the NAM domain. Our data that showed TaNAC TFs responded to fungal disease, which was affected by expression levels and by the regulation of multifarious transcript variants. These data for TaNAC responses to stripe rust and/or powdery mildew and their numerous structural variants provide a good resource for NAC function–mechanism analysis in the context of biotic-stress tolerance in wheat.

Identification and expression analysis of the small auxin-up RNA (SAUR) gene family in apple by inducing of auxin

The small auxin-up RNA (SAUR) family plays a vital role in the regulation of plant growth and development. We identified 80 MdSAUR genes in this study. Phylogenetic analysis indicated that the SAUR proteins from Arabidopsis, rice, and apple were divided into six groups. Of the 80 MdSAURs, 71 were randomly distributed along the 17 chromosomes, while the remaining genes were located along unassigned scafoolds. Among them, a comprehensive overview of SAUR gene family is presented, including gene structures, chromosome locations, duplication and selection pressure analyses, synteny and promoter analyses, and protein interaction. The expression profiles based on microarray data found that 80 genes showed increased expression levels in at least one tissue including seed, seedling, root, stem, leaf, flower, fruit 100daa, and harvested fruit. MdSAUR7 possibly regulate the development of flower organs, and MdSAUR15, MdSAUR24, and MdSAUR80 promote the growth of fruits by regulating cell division. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis indicated the expression levels of 79 MdSAUR genes in leaves under exogenous IAA treatment. MdSAUR4, MdSAUR22, MdSAUR37, MdSAUR38, MdSAUR49, and MdSAUR54 were up-regulated after IAA treatment compared with the control, indicating that they may play specific roles in the IAA signaling transduction pathway. This work provided a foundation for further investigations for the functional analyses of SAURs in apple.

Genome-wide identification and expression analysis of the NAC transcription factor family in tomato (Solanum lycopersicum) during aluminum stress

Background

The family of NAC proteins (NAM, ATAF1/2, and CUC2) represent a class of large plant-specific transcription factors. However, identification and functional surveys of NAC genes of tomato (Solanum lycopersicum) remain unstudied, despite the tomato genome being decoded for several years. This study aims to identify the NAC gene family and investigate their potential roles in responding to Al stress.

Results

Ninety-three NAC genes were identified and named in accordance with their chromosome location. Phylogenetic analysis found SlNACs are broadly distributed in 5 groups. Gene expression analysis showed that SlNACs had different expression levels in various tissues and at different fruit development stages. Cycloheximide treatment and qRT-PCR analysis indicated that SlNACs may aid regulation of tomato in response to Al stress, 19 of which were significantly up- or down-regulated in roots of tomato following Al stress.

Conclusion

This work establishes a knowledge base for further studies on biological functions of SlNACs in tomato and will aid in improving agricultural traits of tomato in the future.

Genome-wide identification and characterization of the soybean SOD family during alkaline stress

Background

Superoxide dismutase (SOD) proteins, as one kind of the antioxidant enzymes, play critical roles in plant response to various environment stresses. Even though its functions in the oxidative stress were very well characterized, the roles of SOD family genes in regulating alkaline stress response are not fully reported.

Methods

We identified the potential family members by using Hidden Markov model and soybean genome database. The neighbor-joining phylogenetic tree and exon-intron structures were generated by using software MEGA 5.0 and GSDS online server, respectively. Furthermore, the conserved motifs were analyzed by MEME online server. The syntenic analysis was conducted using Circos-0.69. Additionally, the expression levels of soybean SOD genes under alkaline stress were identified by qRT-PCR.

Results

In this study, we identified 13 potential SOD genes in soybean genome. Phylogenetic analysis suggested that SOD genes could be classified into three subfamilies, including MnSODs (GmMSD1-2), FeSODs (GmFSD1-5) and Cu/ZnSODs (GmCSD1-6). We further investigated the gene structure, chromosomal locations and gene-duplication, conserved domains and promoter cis-elements of the soybean SOD genes. We also explored the expression profiles of soybean SOD genes in different tissues and alkaline, salt and cold stresses, based on the transcriptome data. In addition, we detected their expression patterns in roots and leaves by qRT-PCR under alkaline stress, and found that different SOD subfamily genes may play different roles in response to alkaline stress. These results also confirmed the hypothesis that the great evolutionary divergence may contribute to the potential functional diversity in soybean SOD genes. Taken together, we established a foundation for further functional characterization of soybean SOD genes in response to alkaline stress in the future.

Genome-Wide Identification and Characterization of the NAC Transcription Factor Family in Musa Acuminata and Expression Analysis during Fruit Ripening

Banana (Musa acuminata, AAA group) is a representative climacteric fruit with essential nutrients and pleasant flavors. Control of its ripening determines both the fruit quality and the shelf life. NAC (NAM, ATAF, CUC2) proteins, as one of the largest superfamilies of transcription factors, play crucial roles in various functions, especially developmental processes. Thus, it is important to conduct a comprehensive identification and characterization of the NAC transcription factor family at the genomic level in M. acuminata. In this article, a total of 181 banana NAC genes were identified. Phylogenetic analysis indicated that NAC genes in M. acuminata, Arabidopsis, and rice were clustered into 18 groups (S1–S18), and MCScanX analysis disclosed that the evolution of MaNAC genes was promoted by segmental duplication events. Expression patterns of NAC genes during banana fruit ripening induced by ethylene were investigated using RNA-Seq data, and 10 MaNAC genes were identified as related to fruit ripening. A subcellular localization assay of selected MaNACs revealed that they were all localized to the nucleus. These results lay a good foundation for the investigation of NAC genes in banana toward the biological functions and evolution.

Genome-wide quantitative trait loci reveal the genetic basis of cotton fibre quality and yield-related traits in a Gossypium hirsutum recombinant inbred line population

Cotton is widely cultivated globally because it provides natural fibre for the textile industry and human use. To identify quantitative trait loci (QTLs)/genes associated with fibre quality and yield, a recombinant inbred line (RIL) population was developed in upland cotton. A consensus map covering the whole genome was constructed with three types of markers (8295 markers, 5197.17 centimorgans (cM)). Six fibre yield and quality traits were evaluated in 17 environments, and 983 QTLs were identified, 198 of which were stable and mainly distributed on chromosomes 4, 6, 7, 13, 21 and 25. Thirty-seven QTL clusters were identified, in which 92.8% of paired traits with significant medium or high positive correlations had the same QTL additive effect directions, and all of the paired traits with significant medium or high negative correlations had opposite additive effect directions. In total, 1297 genes were discovered in the QTL clusters, 414 of which were expressed in two RNA-Seq data sets. Many genes were discovered, 23 of which were promising candidates. Six important QTL clusters that included both fibre quality and yield traits were identified with opposite additive effect directions, and those on chromosome 13 (qClu-chr13-2) could increase fibre quality but reduce yield; this result was validated in a natural population using three markers. These data could provide information about the genetic basis of cotton fibre quality and yield and help cotton breeders to improve fibre quality and yield simultaneously.

Systematic analysis of NAC transcription factors in Gossypium barbadense uncovers their roles in response to Verticillium wilt

As one of the largest plant-specific gene families, the NAC transcription factor gene family plays important roles in various plant physiological processes that are related to plant development, hormone signaling, and biotic and abiotic stresses. However, systematic investigation of the NAC gene family in sea-island cotton (Gossypium babardense L.) has not been reported, to date. The recent release of the complete genome sequence of sea-island cotton allowed us to perform systematic analyses of G. babardense NAC GbNAC) genes. In this study, we performed a genome-wide survey and identified 270 GbNAC genes in the sea-island cotton genome. Genome mapping analysis showed that GbNAC genes were unevenly distributed on 26 chromosomes. Through phylogenetic analyses of GbNACs along with their Arabidopsis counterparts, these proteins were divided into 10 groups (I–X), and each contained a different number of GbNACs with a similar gene structure and conserved motifs. One hundred and fifty-four duplicated gene pairs were identified, and almost all of them exhibited strong purifying selection during evolution. In addition, various cis-acting regulatory elements in GbNAC genes were found to be related to major hormones, defense and stress responses. Notably, transcriptome data analyses unveiled the expression profiles of 62 GbNAC genes under Verticillium wilt (VW) stress. Furthermore, the expression profiles of 15 GbNAC genes tested by quantitative real-time PCR (qPCR) demonstrated that they were sensitive to methyl jasmonate (MeJA) and salicylic acid (SA) treatments and that they could be involved in pathogen-related hormone regulation. Taken together, the genome-wide identification and expression profiling pave new avenues for systematic functional analysis of GbNAC candidates, which may be useful for improving cotton defense against VW.

Systematic analysis of NAC transcription factors' gene family and identification of post-flowering drought stress responsive members in sorghum

SbNAC genes (131) encoding 183 proteins were identified from the sorghum genome and characterized. The expression patterns of SbSNACs were evaluated at three sampling time points under post-flowering drought stress. NAC proteins are specific transcription factors in plants, playing vital roles in development and response to various environmental stresses. Despite the fact that Sorghum bicolor is well-known for its drought-tolerance, it suffers from grain yield loss due to pre and post-flowering drought stress. In the present study, 131 SbNAC genes encoding 183 proteins were identified from the sorghum genome. The phylogenetic trees were constructed based on the NAC domains of sorghum, and also based on sorghum with Arabidopsis and 8 known NAC domains of other plants, which classified the family into 15 and 19 subfamilies, respectively. Based on the obtained results, 13 SbNAC proteins joined the SNAC subfamily, and these proteins are expected to be involved in response to abiotic stresses. Promoter analysis revealed that all SbNAC genes comprise different stress-associated cis-elements in their promoters. UTRs analysis indicated that 101 SbNAC transcripts had upstream open reading frames, while 39 of the transcripts had internal ribosome entry sites in their 5'UTR. Moreover, 298 miRNA target sites were predicted to exist in the UTRs of SbNAC transcripts. The expression patterns of SbSNACs were evaluated in three genotypes at three sampling time points under post-flowering drought stress. Based on the results, it could be suggested that some gene members are involved in response to drought stress at the post-flowering stage since they act as positive or negative transcriptional regulators. Following further functional analyses, some of these genes might be perceived to be promising candidates for breeding programs to enhance drought tolerance in crops.

Transcriptional regulation of osmotic stress tolerance in wheat (Triticum aestivum L.)

The current review provides an updated, new insights into the regulation of transcription mediated underlying mechanisms of wheat plants to osmotic stress perturbations. Osmotic stress tolerance mechanisms being complex are governed by multiple factors at physiological, biochemical and at the molecular level, hence approaches like "OMICS" that can underpin mechanisms behind osmotic tolerance in wheat is of paramount importance. The transcription factors (TFs) are a class of molecular proteins, which are involved in regulation, modulation and orchestrating the responses of plants to a variety of environmental stresses. Recent reports have provided novel insights on the role of TFs in osmotic stress tolerance via direct molecular links. However, our knowledge on the regulatory role TFs during osmotic stress tolerance in wheat remains limited. The present review in its first part sheds light on the importance of studying the role of osmotic stress tolerance in wheat plants and second aims to decipher molecular mechanisms of TFs belonging to several classes, including DREB, NAC, MYB, WRKY and bHLH, which have been reported to engage in osmotic stress mediated gene expression in wheat and third part covers the systems biology approaches to understand the transcriptional regulation of osmotic stress and the role of long non-coding RNAs in response to osmotic stress with special emphasis on wheat. The current concept may lead to an understanding in molecular regulation and signalling interaction of TFs under osmotic stress to clarify challenges and problems for devising potential strategies to improve complex regulatory events involved in plant tolerance to osmotic stress adaptive pathways in wheat.

Comprehensive analysis of NAC transcription factors uncovers their roles during fiber development and stress response in cotton

BACKGROUND

Transcription factors operate as important switches of transcription networks, and NAC (NAM, ATAF, and CUC) transcription factors are a plant-specific family involved in multiple biological processes. However, this gene family has not been systematically characterized in cotton.

RESULTS

Here we identify a large number of genes with conservative NAC domains in four cotton species, with 147 found in Gossypium arboreum, 149 in G. raimondii, 267 in G. barbadense and 283 in G. hirsutum. Predicted membrane-bound NAC genes were also identified. Phylogenetic analysis showed that cotton NAC proteins clustered into seven subfamilies and homologous protein pairs showed similar characteristics. Evolutionary property analysis revealed that purifying selection of NAC genes occurred between diploid and polyploid cotton species, and variation analysis showed GhNAC genes may have been subjected to selection and domestication. NAC proteins showed extensive transactivation and this was dependent on the C-terminus. Some development and stress related cis-elements were enriched in the promoters of GhNAC genes. Comprehensive expression analysis indicated that 38 GhNAC genes were candidates for involvement in fiber development, and 120 in stress responses. Gene co-expression network analysis revealed relationships between fiber-associated NAC genes and secondary cell wall (SCW) biosynthesis genes.

CONCLUSIONS

NAC genes were identified in diploid and tetraploid cotton, revealing new insights into their evolution, variation and homology relationships. Transcriptome analysis and co-expression network indicated roles for GhNAC genes in cotton fiber development and stress response, and NAC genes may prove useful in molecular breeding programmes.

Genome-wide identification and expression profile analysis of the NAC transcription factor family during abiotic and biotic stress in woodland strawberry

The NAC transcription factors involved plant development and response to various stress stimuli. However, little information is available concerning the NAC family in the woodland strawberry. Herein, 37 NAC genes were identified from the woodland strawberry genome and were classified into 13 groups based on phylogenetic analysis. And further analyses of gene structure and conserved motifs showed closer relationship of them in every subgroup. Quantitative real-time PCR evaluation different tissues revealed distinct spatial expression profiles of the FvNAC genes. The comprehensive expression of FvNAC genes revealed under abiotic stress (cold, heat, drought, salt), signal molecule treatments (H2O2, ABA, melatonin, rapamycin), biotic stress (Colletotrichum gloeosporioides and Ralstonia solanacearum). Expression profiles derived from quantitative real-time PCR suggested that 5 FvNAC genes responded dramatically to the various abiotic and biotic stresses, indicating their contribution to abiotic and biotic stresses resistance in woodland strawberry. Interestingly, FvNAC genes showed greater extent responded to the cold treatment than other abiotic stress, and H2O2 exhibited a greater response than ABA, melatonin, and rapamycin. For biotic stresses, 3 FvNAC genes were up-regulated during infection with C. gloeosporioides, while 6 FvNAC genes were down-regulated during infection with R. solanacearum. In conclusion, this study identified candidate FvNAC genes to be used for the genetic improvement of abiotic and biotic stress tolerance in woodland strawberry.

A novel wheat NAC transcription factor, TaNAC30, negatively regulates resistance of wheat to stripe rust

NAC transcription factors are widespread in the plant kingdom and play essential roles in the transcriptional regulation of defense responses. In this study, we isolated a novel NAC transcription factor gene, TaNAC30, from a cDNA library constructed from wheat (Triticum aestivum) plants inoculated with the stripe rust pathogen Puccinia striiformis f. sp. tritici (Pst). TaNAC30 contains a typical NAM domain and localizes to the nucleus. Yeast one-hybrid assays revealed that TaNAC30 exhibits transcriptional activity and that its C-terminus is necessary for the activation of transcription. Expression of TaNAC30 increased when host plants were infected with a virulent race (CYR31) of the rust fungus Pst. Silencing of TaNAC30 by virus-induced gene silencing inhibited colonization of the virulent Pst isolate CYR31. Moreover, detailed histological analyses showed that silencing of TaNAC30 enhanced resistance to Pst by inducing a significant increase in the accumulation of H₂ O₂ . Finally, we overexpressed TaNAC30 in fission yeast and determined that cell viability was severely reduced in TaNAC30-transformed cells grown on medium containing H₂ O₂ . These results suggest that TaNAC30 negatively regulates plant resistance in a compatible wheat-Pst interaction.

Genome-wide analysis and expression profiling of PP2C clade D under saline and alkali stresses in wild soybean and Arabidopsis

Protein phosphatase 2Cs (PP2Cs) belong to the largest protein phosphatase family in plants. Some members have been described as being negative modulators of plant growth and development, as well as responses to hormones and environmental stimuli. However, little is known about the members of PP2C clade D, which may be involved in the regulation of signaling pathways, especially in response to saline and alkali stresses. Here, we identified 13 PP2C orthologs from the wild soybean (Glycine soja) genome. We examined the sequence characteristics, chromosome locations and duplications, gene structures, and promoter cis-elements of the PP2C clade D genes in Arabidopsis and wild soybean. Our results showed that GsPP2C clade D (GsAPD) genes exhibit more gene duplications than AtPP2C clade D genes. Plant hormone and abiotic stress-responsive elements were identified in the promoter regions of most PP2C genes. Moreover, we investigated their expression patterns in roots, stems, and leaves. Quantitative real-time PCR analyses revealed that the expression levels of representative GsPP2C and AtPP2C clade D genes were significantly influenced by alkali and salt stresses, suggesting that these genes might be associated with or directly involved in the relevant stress signaling pathways. Our results established a foundation for further functional characterization of PP2C clade D genes in the future.

Asymmetric Evolution and Expansion of the NAC Transcription Factor in Polyploidized Cotton

Polyploidy in Gossypium hirsutum conferred different properties from its diploid ancestors under the regulation of transcription factors. The NAC transcription factor is a plant-specific family that can be related to plant growth and development. So far, little is known about the NAC family in cotton. This study identified 495 NAC genes in three cotton species and investigated the evolution and expansion of different genome-derived NAC genes in cotton. We revealed 15 distinct NAC subfamilies in cotton. Different subfamilies had different gene proportions, expansion rate, gene loss rate, and orthologous exchange rate. Paleohexaploidization (35%) and cotton-specific decaploidy (32%) might have primarily led to the expansion of the NAC family in cotton. Half of duplication events in G. hirsutum were inherited from its diploid ancestor, and others might have occurred after interspecific hybridization. In addition, NAC genes in the At and Dt subgenomes displayed asymmetric molecular evolution, as evidenced by their different gene loss rates, orthologous exchange, evolutionary rates, and expression levels. The dominant duplication event was different during the cotton evolutionary history. Different genome-derived NACs might have interacted with each other, which ultimately resulted in morphogenetic evolution. This study delineated the expansion and evolutionary history of the NAC family in cotton and illustrated the different fates of NAC genes during polyploidization.

Cotton functional genomics reveals global insight into genome evolution and fiber development

Due to the economic value of natural textile fiber, cotton has attracted much research attention, which has led to the publication of two diploid genomes and two tetraploid genomes. These big data facilitate functional genomic study in cotton, and allow researchers to investigate cotton genome structure, gene expression, and protein function on the global scale using high-throughput methods. In this review, we summarized recent studies of cotton genomes. Population genomic analyses revealed the domestication history of cultivated upland cotton and the roles of transposable elements in cotton genome evolution. Alternative splicing of cotton transcriptomes was evaluated genome-widely. Several important gene families like MYC, NAC, Sus and GhPLDα1 were systematically identified and classified based on genetic structure and biological function. High-throughput proteomics also unraveled the key functional proteins correlated with fiber development. Functional genomic studies have provided unprecedented insights into global-scale methods for cotton research.

The essence of NAC gene family to the cultivation of drought-resistant soybean (Glycine max L. Merr.) cultivars

BACKGROUND

The NAC gene family is notable due to its large size, as well as its relevance in crop cultivation - particularly in terms of enhancing stress tolerance of plants. These plant-specific proteins contain NAC domain(s) that are named after Petunia NAM and Arabidopsis ATAF1/2 and CUC2 transcription factors based on the consensus sequence they have. Despite the knowledge available regarding NAC protein function, an extensive study on the possible use of GmNACs in developing soybean cultivars with superior drought tolerance is yet to be done.

RESULTS

In response to this, our study was carried out, mainly through means of phylogenetic analysis (rice and Arabidopsis NAC genes served as seeding sequences). Through this, 139 GmNAC genes were identified and later grouped into 17 clusters. Furthermore, real-time quantitative PCR was carried out on drought-stressed and unstressed leaf tissues of both sensitive (B217 and H228) and tolerant (Jindou 74 and 78) cultivars. This was done to analyze the gene expression of 28 dehydration-responsive GmNAC genes. Upon completing the analysis, it was found that GmNAC gene expression is actually dependent on genotype. Eight of the 28 selected genes (GmNAC004, GmNAC021, GmNAC065, GmNAC066, GmNAC073, GmNAC082, GmNAC083 and GmNAC087) were discovered to have high expression levels in the drought-resistant soybean varieties tested. This holds true for both extreme and standard drought conditions. Alternatively, the drought-sensitive cultivars exhibited lower GmNAC expression levels in comparison to their tolerant counterparts.

CONCLUSION

The study allowed for the identification of eight GmNAC genes that could be focused upon in future attempts to develop superior soybean varieties, particularly in terms of drought resistance. This study revealed that there were more dehydration-responsive GmNAC genes as (GmNAC004, GmNAC005, GmNAC020 and GmNAC021) in addition to what were reported in earlier inquiries. It is important to note though, that discovering such notable genes is not the only goal of the study. It managed to put emphasis on the significance of further understanding the potential of soybean GmNAC genes, for the purpose of enhancing tolerance towards abiotic stress in general. This scientific inquiry has also revealed that cultivar genotypes tend to differ in their drought-induced gene expression.

ThNAC13, a NAC Transcription Factor from Tamarix hispida, Confers Salt and Osmotic Stress Tolerance to Transgenic Tamarix and Arabidopsis

NAC (NAM, ATAF1/2, and CUC2) proteins play critical roles in many plant biological processes and environmental stress. However, NAC proteins from Tamarix hispida have not been functionally characterized. Here, we studied a NAC gene from T. hispida, ThNAC13, in response to salt and osmotic stresses. ThNAC13 is a nuclear protein with a C-terminal transactivation domain. ThNAC13 can bind to NAC recognized sites and calmodulin-binding NAC (CBNAC) binding element. Overexpression of ThNAC13 in Arabidopsis improved seed germination rate and increased root growth and fresh weight gain under salt or osmotic stress. Transgenic T. hispida plants transiently overexpressing ThNAC13 and with RNAi-silenced ThNAC13 were generated for gain- and loss-of-function experiments. Following exposure to salt or osmotic stress, overexpression of ThNAC13 induced superoxide dismutase (SOD) and peroxidase (POD) activities, chlorophyll and proline contents; decreased the reactive oxygen species (ROS) and malondialdehyde levels; and reduced electrolyte leakage rates in both transgenic Tamarix and Arabidopsis plants. In contrast, RNAi-silenced ThNAC13 showed the opposite results in transgenic Tamarix. Furthermore, ThNAC13 induced the expression of SODs and PODs in transgenic Arabidopsis. These results suggest that ThNAC13 improves salt and osmotic tolerance by enhancing the ROS-scavenging capability and adjusting osmotic potential.

Characterization, Expression, and Functional Analysis of a Novel NAC Gene Associated with Resistance to Verticillium Wilt and Abiotic Stress in Cotton

Elucidating the mechanism of resistance to biotic and abiotic stress is of great importance in cotton. In this study, a gene containing the NAC domain, designated GbNAC1, was identified from Gossypium barbadense L. Homologous sequence alignment indicated that GbNAC1 belongs to the TERN subgroup. GbNAC1 protein localized to the cell nucleus. GbNAC1 was expressed in roots, stems, and leaves, and was especially highly expressed in vascular bundles. Functional analysis showed that cotton resistance to Verticillium wilt was reduced when the GbNAC1 gene was silenced using the virus-induced gene silencing (VIGS) method. GbNAC1-overexpressing Arabidopsis showed enhanced resistance to Verticillium dahliae compared to wild-type. Thus, GbNAC1 is involved in the positive regulation of resistance to Verticillium wilt. In addition, analysis of GbNAC1-overexpressing Arabidopsis under different stress treatments indicated that it is involved in plant growth, development, and response to various abiotic stresses (ABA, mannitol, and NaCl). This suggests that GbNAC1 plays an important role in resistance to biotic and abiotic stresses in cotton. This study provides a foundation for further study of the function of NAC genes in cotton and other plants.

Transcriptome-Wide Identification and Expression Analysis of the NAC Gene Family in Tea Plant [Camellia sinensis (L.) O. Kuntze]

In plants, the NAC (NAM-ATAF1/2-CUC) family of proteins constitutes several transcription factors and plays vital roles in diverse biological processes, such as growth, development, and adaption to adverse factors. Tea, as a non-alcoholic drink, is known for its bioactive ingredients and health efficacy. Currently, knowledge about NAC gene family in tea plant remains very limited. In this study, a total of 45 CsNAC genes encoding NAC proteins including three membrane-bound members were identified in tea plant through transcriptome analysis. CsNAC factors and Arabidopsis counterparts were clustered into 17 subgroups after phylogenetic analysis. Conserved motif analysis revealed that CsNAC proteins with a close evolutionary relationship possessed uniform or similar motif compositions. The distribution of NAC family MTFs (membrane-associated transcription factors) among higher plants of whose genome-wide has been completed revealed that the existence of doubled TMs (transmembrane motifs) may be specific to fabids. Transcriptome analysis exhibited the expression profiles of CsNAC genes in different tea plant cultivars under non-stress conditions. Nine CsNAC genes, including the predicted stress-related and membrane-bound genes, were examined through qRT-PCR (quantitative real time polymerase chain reaction) in two tea plant cultivars, namely, 'Huangjinya' and 'Yingshuang'. The expression patterns of these genes were investigated in different tissues (root, stem, mature leaf, young leaf and bud) and under diverse environmental stresses (drought, salt, heat, cold and abscisic acid). Several CsNAC genes, including CsNAC17 and CsNAC30 that are highly orthologous to known stress-responsive ANAC072/RD26 were identified as highly responsive to abiotic stress. This study provides a global survey of tea plant NAC proteins, and would be helpful for the improvement of stress resistance in tea plant via genetic engineering.

GhATAF1, a NAC transcription factor, confers abiotic and biotic stress responses by regulating phytohormonal signaling networks

Dual function of GhATAF1 in the responses to salinity stress and Verticillium dahliae infection in cotton. NAC (NAM/ATAF1/2/CUC2) is a large plant-specific transcription factor family that plays important roles in the response to abiotic stresses. We previously isolated a cotton NAC transcription factor gene, GhATAF1, which was up-regulated by ABA, cold and salt stresses and classified into AFAT1/2, a sub-family of NAC. Here, we report that GhATAF1 was also highly induced by MeJA, SA and Verticillium dahliae inoculation, which implied that GhATAF1 was involved not only in the response to abiotic stress but also in the response to biotic stress. GhATAF1 was localized in the nucleus and possessed transactivation activity. Overexpression of GhATAF1 enhanced cotton plant tolerance to salt stress by enhancing the expression of various stress-related genes, including the ABA response gene GhABI4; the transporter gene GhHKT1, involved in Na(+)/K(+) homeostasis; and several stress-response genes (GhAVP1, GhRD22, GhDREB2A, GhLEA3, and GhLEA6). Additionally, overexpressing GhATAF1 increased cotton plant susceptibility to the fungal pathogens V. dahliae and Botrytis cinerea, coupled with the suppression of JA-mediated signaling and the activation of SA-mediated signaling. Our results suggested that GhATAF1, the cotton stress-responsive NAC transcription factor, plays important roles in the response to both abiotic stress and biotic stress by coordinating the phytohormone signaling networks.

Genome-scale analysis of the cotton KCS gene family revealed a binary mode of action for gibberellin A regulated fiber growth

Production of β-ketoacyl-CoA, which is catalyzed by 3-ketoacyl-CoA synthase (KCS), is the first step in very long chain fatty acid (VLCFA) biosynthesis. Here we identified 58 KCS genes from Gossypium hirsutum, 31 from G. arboreum and 33 from G. raimondii by searching the assembled cotton genomes. The gene family was divided into the plant-specific FAE1-type and the more general ELO-type. KCS transcripts were widely expressed and 32 of them showed distinct subgenome-specific expressions in one or more cotton tissues/organs studied. Six GhKCS genes rescued the lethality of elo2Δelo3Δ yeast double mutant, indicating that this gene family possesses diversified functions. Most KCS genes with GA-responsive elements (GAREs) in the promoters were significantly upregulated by gibberellin A3 (GA). Exogenous GA3 not only promoted fiber length, but also increased the thickness of cell walls significantly. GAREs present also in the promoters of several cellulose synthase (CesA) genes required for cell wall biosynthesis and they were all induced significantly by GA3 . Because GA treatment resulted in longer cotton fibers with thicker cell walls and higher dry weight per unit cell length, we suggest that it may regulate fiber elongation upstream of the VLCFA-ethylene pathway and also in the downstream steps towards cell wall synthesis.

Expression of GhNAC2 from G. herbaceum, improves root growth and imparts tolerance to drought in transgenic cotton and Arabidopsis

NAC proteins are plant-specific transcription factors that play essential roles in regulating development and responses to abiotic and biotic stresses. We show that over-expression of the cotton GhNAC2 under the CaMV35S promoter increases root growth in both Arabidopsis and cotton under unstressed conditions. Transgenic Arabidopsis plants also show improved root growth in presence of mannitol and NaCl while transgenic cotton expressing GhNAC2 show reduced leaf abscission and wilting upon water stress compared to control plants. Transgenic Arabidopsis plants also have larger leaves, higher seed number and size under well watered conditions, reduced transpiration and higher relative leaf water content. Micro-array analysis of transgenic plants over-expressing GhNAC2 reveals activation of the ABA/JA pathways and a suppression of the ethylene pathway at several levels to reduce expression of ERF6/ERF1/WRKY33/ MPK3/MKK9/ACS6 and their targets. This probably suppresses the ethylene-mediated inhibition of organ expansion, leading to larger leaves, better root growth and higher yields under unstressed conditions. Suppression of the ethylene pathway and activation of the ABA/JA pathways also primes the plant for improved stress tolerance by reduction in transpiration, greater stomatal control and suppression of growth retarding factors.

Genome-Wide Identification of R2R3-MYB Genes and Expression Analyses During Abiotic Stress in Gossypium raimondii

The R2R3-MYB is one of the largest families of transcription factors, which have been implicated in multiple biological processes. There is great diversity in the number of R2R3-MYB genes in different plants. However, there is no report on genome-wide characterization of this gene family in cotton. In the present study, a total of 205 putative R2R3-MYB genes were identified in cotton D genome (Gossypium raimondii), that are much larger than that found in other cash crops with fully sequenced genomes. These GrMYBs were classified into 13 groups with the R2R3-MYB genes from Arabidopsis and rice. The amino acid motifs and phylogenetic tree were predicted and analyzed. The sequences of GrMYBs were distributed across 13 chromosomes at various densities. The results showed that the expansion of the G. Raimondii R2R3-MYB family was mainly attributable to whole genome duplication and segmental duplication. Moreover, the expression pattern of 52 selected GrMYBs and 46 GaMYBs were tested in roots and leaves under different abiotic stress conditions. The results revealed that the MYB genes in cotton were differentially expressed under salt and drought stress treatment. Our results will be useful for determining the precise role of the MYB genes during stress responses with crop improvement.

Genome-wide analysis, expression dynamics and varietal comparison of NAC gene family at various developmental stages in Morus notabilis

NAC genes are important transcription factors and forms a large family in plants. They have shown to play an important role in growth and development and have also been shown to involve in regulation of stress-responsive genes. In the present study, a repertoire of NAC genes in recently published mulberry genome has been identified which consists of a total of 79 members. Structural analysis revealed that most of the NAC genes in mulberry contain two introns. The proteins encoded by them show a wide range of isoelectric points suggestive of their varied roles in varying microcellular environment. Phylogenetic and conserved motif analysis elucidate the presence of 15 sub-groups of these genes along with two novel sub-groups having distinct conserved motifs which are not present in Arabidopsis. Gene ontology term enrichment analysis and cis-element identification from their putative 1 K upstream regulatory region indicates their possible role in important biological processes like organ formation, meristem establishment, senescence, and various biotic and abiotic stresses. Expression analysis across various developmental stages led to identification of their preferential expression in diverse tissues. Taken together, this work provides a solid background information related to structure, function, expression and evolution of NAC gene family in mulberry.

Cotton GhMYB7 is predominantly expressed in developing fibers and regulates secondary cell wall biosynthesis in transgenic Arabidopsis

The secondary cell wall in mature cotton fibers contains over 90% cellulose with low quantities of xylan and lignin. However, little is known regarding the regulation of secondary cell wall biosynthesis in cotton fibers. In this study, we characterized an R2R3-MYB transcription factor, GhMYB7, in cotton. GhMYB7 is expressed at a high level in developing fibers and encodes a MYB protein that is targeted to the cell nucleus and has transcriptional activation activity. Ectopic expression of GhMYB7 in Arabidopsis resulted in small, curled, dark green leaves and also led to shorter inflorescence stems. A cross-sectional assay of basal stems revealed that cell wall thickness of vessels and interfascicular fibers was higher in transgenic lines overexpressing GhMYB7 than in the wild type. Constitutive expression of GhMYB7 in Arabidopsis activated the expression of a suite of secondary cell wall biosynthesis-related genes (including some secondary cell wall-associated transcription factors), leading to the ectopic deposition of cellulose and lignin. The ectopic deposition of secondary cell walls may have been initiated before the cessation of cell expansion. Moreover, GhMYB7 was capable of binding to the promoter regions of AtSND1 and AtCesA4, suggesting that GhMYB7 may function upstream of NAC transcription factors. Collectively, these findings suggest that GhMYB7 is a potential transcriptional activator, which may participate in regulating secondary cell wall biosynthesis of cotton fibers.

Comprehensive analysis of NAC transcription factors in diploid Gossypium: sequence conservation and expression analysis uncover their roles during fiber development

Determining how function evolves following gene duplication is necessary for understanding gene expansion. Transcription factors (TFs) are a class of proteins that regulate gene expression by binding to specific cis-acting elements in the promoters of target genes, subsequently activating or repressing their transcription. In the present study, we systematically examined the functional diversification of the NAC transcription factor (NAC-TFs) family by analyzing their chromosomal location, structure, phylogeny, and expression pattern in Gossypium raimondii (Gr) and G. arboreum (Ga). The 145 and 141 NAC genes identified in the Gr and Ga genomes, respectively, were annotated and divided into 18 subfamilies, which showed distinct divergence in gene structure and expression patterns during fiber development. In addition, when the functional parameters were examined, clear divergence was observed within tandem clusters, which suggested that subfunctionalization had occurred among duplicate genes. The expression patterns of homologous gene pairs also changed, suggestive of the diversification of gene function during the evolution of diploid cotton. These findings provide insights into the mechanisms underlying the functional differentiation of duplicated NAC-TFs genes in two diploid cotton species.